Is There an Edge to Evolution? Part 3

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October 23, 2010 Tags: Design

Today's entry was written by David Ussery. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Is There an Edge to Evolution? Part 3

In his previous post, Dr. Ussery showed that Behe’s analysis of the probability of getting beneficial mutations is flawed at fundamental levels. Beneficial mutations do occur, new genes do evolve and he cited some research articles that demonstrate this and then showed the interested reader how to gain access to the vast scientific literature that exists. He expresses concern that Michael Behe has not chosen to make the general public aware of what is being done in this arena.

In today’s post he goes on to examine what Behe states is the limit of what Darwinian evolution can and cannot do.

Chapter 4 - What Darwinism Can Do

The title for this chapter is a bit deceptive, in that most of this chapter is not really about what evolution CAN do, but rather what the limits to evolution are (the topic for the next chapter). There is a short description of genome sequence analysis and the types of mutations observed in the laboratory, but in my opinion this chapter is really missing a thorough discussion of the astounding variety and diversity we find when we examine genomes.

Again, Behe emphasizes that he has no problem with evolution by common descent:

Over the next few sections I'll show some of the newest evidence from studies of DNA that convinces most scientists, including myself, that one leg of Darwin's theory - common descent - is correct. (page 65).

Once again, the problem is random mutations:

The bottom line is this. Common descent is true; yet the explanation of common descent – even the common descent of humans and chimps – although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities come from, or how humans subsequently acquired remarkable differences. Something nonrandom must account for the common descent of life. (page 65, emphasis in the original).

I absolutely agree with Behe – there must be a ‘non-random’ account. But I’m a bit confused here, because natural selection is, by definition, definitely non-random. That’s the whole point! There is (random) variation, and then those variants that are better are selected. It is not at all random. But Behe’s claim here is that there are not enough random variants produced for evolution to occur. 150 years ago, at the time of Darwin’s writing, it was not known whether the variation was random or produced in some other manner – and in a sense this did not matter.

What was important for Darwin was that the variation was there, and that the method for non-random selection – also known as “natural selection” – could account for the non-random common descent of life. One of the analogies Darwin used was “artificial selection”, where, for example, dog breeders would breed certain traits, giving rise to a large variety of dogs within a short amount of time – merely by [non-randomly] selecting for desired traits. Darwin reasoned if this worked for breeders, why couldn’t it work in natural environments? And as far as “random variations” go, we have quite a bit of variance in dogs, from tiny toy poodles to St. Bernards.

More than half the chapter is devoted to species that have had duplications of their entire genome. Behe focuses especially on yeast, although he mentions in a footnote that other whole genome duplications have been documented. But again, the text written is more within the framework of the limits of evolution—what it can’t do, which should be the subject for the next chapter (I suspect a chapter strictly about what Behe thought evolution could do would be quite thin). The claim that “genome duplication…. has not given baker’s yeast any advantage it wouldn’t otherwise have had” (page 74) seems pretty harsh, especially now that more than two dozen different strains of yeast have been sequenced, and there are clear advantages in survival associated with duplication of many of these genes.

Perhaps, once again, Behe is not familiar with the literature and not willing to have a look at what has been published. I encourage the interested reader to go ahead and have a look at what is out there—go to PubMed, and type in the words “yeast genome duplication evolution” and have a look at the articles found. Today when I did this, I found 420 articles. The second one on the list has this statement in the concluding sentence of the abstract: “Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles.” Behe concludes the chapter by saying that “although Darwin hoped otherwise, random variation doesn't explain the most basic features of biology” (page 83).

For more on what evolution CAN do, I mention “The Edge of Evolution” in a footnote in the last chapter (Evolution of Microbial Communities) of my textbook on Comparative Genomics. It is in a section on “Where Does Diversity Come From?”, and I make the statement that some anti-evolutionists “claim that there is not enough diversity in bacterial populations for evolution to occur.” I encourage the interested reader to have a look at this section, as I think it is a nice culmination of a story I’ve slowly built up through the previous chapters on bacterial genomics.

I readily admit that this is something that takes time to understand and cannot easily be explained in a 10-second sound bite – this textbook came from a course I’ve taught at the Technical University of Denmark since 2000. Currently the course meets in the autumn semester, for 8 hours a week, for 13 weeks; this year I have 54 students. So this takes time to explain, but my point here is that the claim that nothing has changed over the past 10 years, in terms of evidence for evolution and documented diversity, is simply wrong.

Chapter 5 - What Darwinism Can't Do

The title of this chapter reminds me of a book by Lenny Moss, called What Gene’s Can’t Do. I think this is a wonderful book, kind of countering the “gene-centric” popular culture. It’s a well-written book, and in my opinion he makes some valid scientific points. Unfortunately, although Behe could have had a similar good discussion here, instead we are treated to poor quality left-overs. This chapter is kind of an update on “irreducible complexity” as outlined in Behe's previous book, Darwin's Black Box. In spite of strong protestations from many (including myself) in their reviews of that work, Behe still clings to the idea that no one has ever published anything about the evolution of these complex molecular machines. “Despite the amazing advance of molecular biology as a whole, despite the sequencing of hundreds of entire genomes and other leaps in knowledge, despite the provocation of Darwin's Black Box itself, in the more than ten years since I pointed out that a situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged” (page 95).

Again, the interested reader is invited to visit PubMed, type in “cilium evolution” and see for oneself: are we to believe that articles with titles like “The evolution of the cilium and the eukaryotic cell” and 'Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis” simply don't exist? Perhaps if one closes their eyes, and clicks their heels three times, thinking, “They don't exist, they don't exist”, maybe these articles can simply vanish!

Last week I gave a lecture in my course about the 10th anniversary of sequencing the human genome. In the field of genomics, much has happened in the past 10 years. There has been an explosion in the amount of genomic data available, and also in the strong, clear evidence for evolution in exactly the manner Behe claims is impossible and will never happen. To put this in perspective – when I first came to the Center for Biological Sequence Analysis in 1997, there were four bacterial genomes sequenced. Last week, in my course I showed an update of the currently sequenced genomes: there are now more than four thousand genomes sequenced, and the number is growing on a daily basis. And the more genomes we sequence, the more we learn about how evolution works. When I was growing up, the preacher in our church used to say, “Did you hear about the guy who said ‘It can’t be done?’ Well he got run over by the guy doing it!” I think there is some truth in this – Behe says it can’t be done, and a decade later, despite this vast amount of data, he claims things remain “utterly unchanged”.

In my next post, I will examine Behe’s discussion of whether random mutation hitched to natural selection is a biological explanation for various molecular phenomena.


David Ussery is an associate professor of comparative microbial genomics at the Center for Biological Sequence Analysis at the Technical University of Denmark and on the faculty at the University in Oslo, Norway. Ussery is the co-author of Computing for Comparative Microbial Genomics and has authored or co-authored 130 articles for science and professional journals. He is also a frequent public speaker on the topic of bacterial genomics.

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Bilbo - #36005

October 23rd 2010

Comment removed by moderator.


pds - #36006

October 23rd 2010

“Again, the interested reader is invited to visit PubMed, type in “cilium evolution” and see for oneself: are we to believe that articles with titles like “The evolution of the cilium and the eukaryotic cell” and ‘Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis” simply don’t exist? “

PubMed searches and titles is all you can do?  The question is what do these show.  Misleading generalizations about Behe’s arguments and reference to PubMed titles will not convince me.  A discussion of what the articles establish, and the evidence relied on is what will be convincing for me.

“Behe still clings to the idea that no one has ever published anything about the evolution of these complex molecular machines.”

That’s not what he says.  Again, a straw man.

“Behe says it can’t be done.”

That oversimplifies what he says.  He looks at what has been shown, he considers possible evolutionary pathways, he weighs plausibility, and he draws certain inferences.  You have not shown that his inferences are wrong.


beaglelady - #36007

October 23rd 2010

I’ve found this series to be very informative. Thank you very much.


gingoro - #36008

October 23rd 2010

Good series, not unrelated to what Steve Mathison has written about Behe on Steve’s blog.


Dave Ussery - #36024

October 23rd 2010

pds - #36006 - PubMed searches and titles is all you can do?

———————

YES, I can do much more than PubMed searches - actually, if you take a deep breath, and actually read what I’ve written at the end of the section on Chapter 4, I say that I have developed these ideas in the form of a full-length textbook, and I CANNOT give an explanation in 10 seconds…


Tim - #36028

October 23rd 2010

PDS,

I would say that Behe’s inferences were demonstrably wrong concerning the bacterial flagellum and the blood clotting cascade being irreducibly complex.


conrad - #36036

October 23rd 2010

Non random….... that is the key.

All of these “quantum events” and things that “just happen” according to Heisenberg’s uncertainty principle,..... THAT IS THE LORD IN ACTION!

Albert Einstein said,    “Coincidence is God’s way of remaining anonymous.”


sy - #36049

October 23rd 2010

Here is an abstract of a paper.

J Cell Sci. 2010 May 1;123(Pt 9):1407-13.
Reconstructing the evolutionary history of the centriole from protein components.
Hodges ME,et al.
Centrioles are highly conserved structures that fulfil important cellular functions, such as nucleation of cilia and flagella (basal-body function) and organisation of pericentriolar material to form the centrosome. The evolution of these functions can be inferred from the distribution of the molecular components of extant centrioles and centrosomes. Here, we undertake an evolutionary analysis of 53 proteins known either for centriolar association or for involvement in cilia-associated pathologies. By linking protein distribution in 45 diverse eukaryotes with organism biology, we provide molecular evidence to show that basal-body function is ancestral, whereas the presence of the centrosome is specific to the Holozoa. We define an ancestral centriolar inventory of 14 core proteins, Polo-like-kinase, and proteins associated with Bardet-Biedl syndrome (BBS) and Meckel-Gruber syndrome. We show that the BBSome is absent from organisms that produce cilia only for motility, predicting a dominant and ancient role for this complex in sensory function.


sy - #36050

October 23rd 2010

The rest of the abstract follows

We also show that the unusual centriole of Caenorhabditis elegans is highly divergent in both protein composition and sequence. Finally, we demonstrate a correlation between the presence of specific centriolar proteins and eye evolution. This correlation is used to predict proteins with functions in the development of ciliary, but not rhabdomeric, eyes.

I think this paper nicely represents the sort of work that has been done on the origins of ciliar components.


beaglelady - #36058

October 23rd 2010

...actually, if you take a deep breath, and actually read what I’ve written at the end of the section on Chapter 4, I say that I have developed these ideas in the form of a full-length textbook…

What a notion, Dr. Ussery! Actually reading your entire article before commenting!


conrad - #36078

October 24th 2010

Well the enviromental niche determines the organism that will live there.

Who creates the niche?
Well it ain’t Behe or Jerry Coyne.
So why do we spend so much time on those two guys?


pds - #36095

October 24th 2010

Dave U.,

You said:

>>>pds - #36006 - PubMed searches and titles is all you can do?

———————

YES, I can do much more than PubMed searches - actually, if you take a deep breath, and actually read what I’ve written at the end of the section on Chapter 4, I say that I have developed these ideas in the form of a full-length textbook, and I CANNOT give an explanation in 10 seconds…<<<

******

I thought it was clear, but I was looking something more than 10 seconds and less than a textbook.  For example, a blog series.  Are you saying that to get your real convincing critique of Behe I have to buy your textbook?  You cannot summarize specific studies that refute specific arguments that Behe makes?  OK, I get it.


pds - #36097

October 24th 2010

(cont.)

I looked at your textbook on Google books, like you invited.  You mention Edge of Evolution in a footnote, call Behe a “creationist” and misrepresent his argument (again).  You say, “some creationists who oppose evolution claim that there is not enough diversity in bacterial populations for evolution to occur.”  That is not Behe’s argument.

If you quote Behe accurately, everyone could see that he is looking for “a Darwinian explanation for the step-by-step origin of the cilium.”  p. 95.  Surely you can summarize a study that does this? Perhaps just the first three to five steps of the step by step sequence, and the survival advantage of each?


Gregory - #36099

October 24th 2010

Do you really directly call Behe a ‘creationist’, David Ussery?!

What a shame that would be.

In light of this ‘evidence,’ if it is true what pds has uncovered, it is only fair to return to you a question from early in this thread, which David seemed to dodge with distaste and posturing.

Do you or do you not, David Ussery, consider yourself a ‘Darwinist’? YES or NO?

I would find it impossible for you to be an ‘objective’ or ‘impartial’ observer on the topic of ‘limits to Darwinism’ if you consider yourself a Darwinist. You simply would be deemed, and lawfully so, unable to come up with legitimate *limits to Darwinism* if this were the case and your pseudo-critique would be assessed by readers in this light.

Please don’t dodge this direct and simple question by trying to express doubt about what Darwinism means. It is a yes or no question only. There is no ‘maybe’ answer here.


gingoro - #36104

October 24th 2010

Gregory @36099

“Do you really directly call Behe a ‘creationist’,”
I would hope that Behe is a creationist just like Denis Lamoureux and I am.  After all Denis calls himself an Evolutionary Creationist.  What I doubt is that Behe or any of the rest of us are young earth creationists.  Now if Ussery meant that Behe is YEC, that is obviously false and defamatory.  If Ussery meant that Behe allows no place for evolution and that God directly created the species, that also seems to me to be false.  Thus in my opinion we need to understand what Ussery meant.
Dave W


Karl A - #36105

October 24th 2010

Gregory, I sure wish you would write a blog post or (better) a scholarly article bringing your perspectives to bear, particularly wrt evolutionism.  I find your brief posts tantalizing but often cryptic.  Maybe a critique of something E.O. Wilson has written would be a useful scaffolding (or foil) for your ideas.

On the topic at hand, is Behe a creationist?  Well, yes, I think he is.  Most of us here are small-c creationists, if we believe God is behind this old universe of ours.  I hope Dr. Usser considers himself one of these.  Is Behe a (large C) Creationist?  I thought the definition of Creationist was one who believes in a substantial number of “poofing” miracles to get things the way they are now.  If Behe is a Creationist, I guess I (evolutionary creationist) am too. While I don’t know if science can conclusively point to God’s creative activity, I certainly believe God has been actively involved and won’t rule out that at some point he may have left fingerprints.

Have I missed something that somehow does not make this (labeling Behe an evolution-opposing creationist) a minor scandal?


Rich - #36106

October 24th 2010

Tim:

Presumably you would not say that Behe is wrong regarding the neo-Darwinian evolvability of the bacterial flagellum unless you were capable of providing a hypothetical neo-Darwinian pathway from a bacterium without a flagellum to a bacterium with one.

Well, let’s have it.


Karl A - #36121

October 24th 2010

P.S. I posted my comment before Dave W’s showed up, hence the duplication.


Rich - #36133

October 24th 2010

beaglelady:

“What a notion, Dr. Ussery! Actually reading your entire article before commenting!”

Hear, hear!  Now if only a number of anti-ID commenters on this site would follow that wise advice, and actually carefully read a substantial amount of ID theory before rejecting it!

(No, I’m not speaking of Dr. Ussery.  Those referred to know who they are.)

By the way, beaglelady, you mentioned that you wanted to read a new book by Robert Pennock.  After you read it, you might want to read the criticism of Pennock by Dr. Bradley Monton, also like Pennock a professor of philosophy.  Monton is an atheist, and therefore cannot be accused of explaining the origin of species by “Poof!”  But Monton, unlike Pennock, keeps an open mind about ID, and in his new book he directly criticizes Pennock’s thought about the nature of science and his performance in the Dover Trial.  Monton also discusses Pennock’s apparent attempt to academically intimidate him.  For the book, and a relevant web discussion, see:

*Seeking God in Science: An Atheist Defends Intelligent Design* (Broadview, 2009)

http://bradleymonton.wordpress.com/category/pennock/

http://intelligentdesign.podomatic.com/player/web/2010-09-22T16_37_13-07_00


defensedefumer - #36135

October 24th 2010

Good post, Dr Ussery!

After hearing about nylon-digesting Flavobacterium and citrate-absorbing E.coli, my views of God and science shifted away from irreducible complexity.

I do wonder if there is a limit to evolution though—I know that all organisms are limited by their current environment and evolutionary history, but is there anything concrete that evolution cannot do (like humans evolving gills or wings)?

I’m pumped for the next post!


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